Audit Scotland found the proportion of patients marked as “socially unavailable” to attend appointments had risen from 11 per cent to more than 30 per cent as ministers imposed more stringent deadlines.

Scotland’s GPs led the backlash against SNP ministers by arguing the report illustrated how patient care was being compromised by politically motivated targets.

Although the NHS is supposed to provide treatment within a specified number of weeks, the period that patients are classified as unavailable does not count towards their waiting times.

While official figures showed only three per cent of in-patients were waiting longer than the target nine weeks in June 2011, auditors found that the real figure was 23 per cent when periods of ‘unavailability’ were included.

Audit Scotland could not state definitively that boards had deliberately fiddled the system to meet their targets because there are few records stating why patients were deemed to be unavailable.

However, the report noted that health boards started reducing the number of people classified as unavailable after one, NHS Lothian, was caught manipulating waiting lists.

It criticised Nicola Sturgeon, the former Health Minister, for failing to question how waiting lists were being cut or why the number of patients deemed unavailable was increasing so rapidly.

Alex Neil, her successor, said today’s report showed there were no other examples of waiting lists being fiddled and insisted patients are being treated quicker than ever.

But the British Medical Association (BMA) in Scotland, representing GPs, attacked the focus on targets and opposition parties argued that thousands of patients had their treatment delayed as a consequence.

Dr Brian Keighley, the BMA’s chairman in Scotland, said the systems monitoring waiting times are “inadequate and have been open to manipulation.”

“This is not in the best interests of the patient, and largely the result of the drive for political point scoring in our NHS. The BMA has often voiced its concern that certain politically motivated targets can skew clinical priorities,” he said.

Jackie Baillie, Scottish Labour health spokesman, said: “This report makes clear that hidden waiting lists were widespread, not just in Lothian and the SNP government was aware there was a problem and did nothing.”

Health boards are permitted to classify patients as socially unavailable for treatment if, for example, they go on holiday or they choose to wait longer to be seen locally.

When this occurs, the report said the patient's “clock stops” and the period they are unavailable is not included in the reported waiting time.

As Health Minister, Ms Sturgeon gradually reduced NHS targets until they reached a maximum of 18 weeks wait from a patient being referred by a GP to the start of treatment.

Audit Scotland found that as targets shortened, the proportion of patients designated unavailable for treatment increased from 11 per cent in 2008 to more than 30 per cent in mid-2011.

The figures started dropping from the end of 2011, the report said, “around the time manipulation of waiting lists was found in NHS Lothian.”

Auditors said that generally NHS staff did not record the reason patients were listed as unavailable, thereby making it impossible to tell whether the classification was valid.

However, they said the result was patients’ actual waits were longer than those reported in official figures.

For example, Forth Valley reported in June 2011 that only two per cent of in-patients had been forced to wait more than nine weeks for treatment.

But auditors said the real figure was 37 per cent when periods of supposed ‘unavailability’ were included.

Three hundred people on waiting lists in NHS Grampian last year had four or more periods when they were designated as being unavailable.

NHS Highland placed people on an ‘unavailable list’ indefinitely, auditors found, with two records of ophthalmology patients being classed as such for more than a year.

Caroline Gardner, Auditor General for Scotland, said: “NHS boards and the Scottish government must improve the monitoring of boards’ use of waiting list codes if they are to retain public trust and assure patients they are being treated fairly.”

But Mr Neil insisted most of the report’s recommendations are already being implemented. He added: “Let us not forget the most important thing – that waiting times are amongst their lowest ever levels in Scotland and they continue to improve.”